"The prosecutors' office sought a ban on leaving the country for President Otto Perez, and Judge Miguel Angel Galvez ordered it", prosecutors said on Twitter.
Congress voted to strip Perez's immunity, which clears the way for him to be prosecuted over allegations he masterminded a multi-million-dollar corruption scheme.
The resolution was passed unanimously by the 132 lawmakers present, making the conservative leader the first president to have his immunity revoked in the Central American country's history.
After months of unprecedented protests that have swept Guatemala, hundreds of demonstrators outside Congress erupted into jubilant cheers at the news, as passing drivers honked their horns in celebration.
The vote clears the way for prosecutors to charge Perez, a 64-year-old retired general, with running a scheme that allowed businesses to reduce their customs duty by paying bribes to corrupt officials.
Under Guatemalan law, he will be automatically removed from office if remanded in custody by a judge.
Perez's lawyers filed a motion Monday challenging the immunity vote before the Constitutional Court, which is expected to rule by Thursday.
The scandal, which has already felled his former vice president and a string of top officials, comes as Guatemala prepares for elections Sunday to choose Perez's successor.
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